Structure and function of phage RNA.
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Base Sequence↗
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Longitudinal phenotypic analysis of human immunodeficiency virus type 1-specific cytotoxic T lymphocytes: correlation with disease progression.
Few studies have examined longitudinal changes in human immunodeficiency virus type 1 (HIV)-specific cytotoxic T lymphocytes (CTL). To more closely define the natural history of HIV-specific CTL, we used HLA-peptide tetrameric complexes to study the longitudinal CD8(+) T-cell response evolution in 16 A*0201-positive untreated individuals followed clinically for up to 14 years. As early as 1 to 2 years after seroconversion, we found a significant association between high frequencies of A*0201-restricted p17(Gag/Pol) tetramer-binding cells and slower disease progression (P < 0.01). We observed that responses could remain stable over many months, but any longitudinal changes that occurred were typically accompanied by reciprocal changes in RNA viral load. Phenotypic analysis with markers CD45RO, CD45RA, and CD27 identified distinct subsets of antigen-specific cells and the preferential loss of CD27(+) CD45RO(+) cells during periods of rapid decline in the frequency of tetramer-binding cells. In addition we were unable to confirm previous studies showing a consistent selective loss of HIV-specific cells in the context of sustained Epstein-Barr virus-specific cell frequencies. Overall, these data support a role of HIV-specific CTL in the control of disease progression and suggest that the ultimate loss of such CTL may be preferentially from the CD27(+) CD45RO(+) subset.
Disease Progression↗
Seminal reservoirs during an HIV type 1 eradication trial.
Despite dramatic reduction of the levels of human immunodeficiency virus type I (HIV-1) virions in blood and seminal plasma of infected patients, highly active antiretroviral therapy (HAART) does not eradicate HIV-1. Three patients, with less than 50 copies/ml of plasma viral RNA, were enrolled in this eradication protocol. Didanosine (DDI) and hydroxyurea (HU) were added to their baseline HAART and after a month of therapy, low dose OKT3, followed by a 2-week course of interleukin 2 (IL-2), was administrated. All antiretroviral therapy was then interrupted and the three patients developed viral rebound in the peripheral blood. The V3 loop region of the HIV-1 gp120 from cell-free viral RNA and proviral DNA in blood and seminal compartments was sequenced in one patient. The two major viral isolates in semen cells were macrophage- tropic (R5) and dual-tropic (R5X4), and these isolates were also present in the PBMCs. Six months after the viral rebound, we demonstrated a shift toward dual tropism in semen cell-associated HIV-1 proviral DNA, with the first appearance of a T-lymphotropic (X4) provirus solely in this compartment. The virus responsible for the blood plasma viral rebound was never found in the semen microenvironment. This study suggests viral compartmentalization of the semen microenvironment after an intensification and stimulatory HIV-1 eradication protocol, with evidence of viral evolution.
Amino Acid Sequence↗
Molecular evolution of puumala hantavirus in Fennoscandia: phylogenetic analysis of strains from two recolonization routes, Karelia and Denmark.
Like other members of the genus HANTAVIRUS: in the family BUNYAVIRIDAE:, Puumala virus (PUUV) is thought to be co-evolving with its natural host, the bank vole Clethrionomys glareolus. To gain insight into the evolutionary history of PUUV in northern Europe during the last post-glacial period, we have studied wild-type PUUV strains originating from areas along two postulated immigration routes of bank voles to Fennoscandia. Full-length sequences of the S RNA segment and partial sequences (nt 2168-2569) of the M segment were recovered by RT-PCR directly from bank vole tissues collected at three locations in Russian Karelia and one location in Denmark. Phylogenetic analysis showed that strains from Karelia and Finland belong to the same genetic lineage, supporting the hypothesis that PUUV spread to present Finland via a Karelian land-bridge. The Danish PUUV strains showed no particularly close relatedness to any of the known PUUV strains and formed a distinct phylogenetic lineage on trees calculated for both S and M segment sequences. Although no direct link between the Danish PUUV strains and those of the southern Scandinavian lineage was found, within the S segment of Danish PUUV strains, two regions with higher similarity to either northern Scandinavian or - to a less extent - southern Scandinavian genetic lineages were revealed, suggesting evolutionary connections of their precursors.
Amino Acid Sequence↗
Limitations to tobacco mosaic virus infection of turnip.
Turnip vein-clearing virus (TVCV) and tobacco mosaic virus (TMV) represent subgroups of tobamoviruses infecting cruciferous and solanaceous plants, respectively. To identify adaptations that may have been necessary in the evolution of the TVCV subgroup from a TMV-like ancestor, the infection of turnip plants by TMV and by chimeras between TMV and TVCV was explored. TMV accumulated at spatially limited sites on inoculated turnip leaves as determined by leaf skeleton hybridization. A plasmid DNA containing a complete TVCV cDNA, when transcribed in vitro, produced RNA that was infectious to tobacco and turnip plants. TVCV-TMV chimeric genomes with junctions within coding regions were not infectious to tobacco, though the movement protein (MP) chimera was infectious to tobacco with a TMV MP transgene. Reciprocal chimeras with junctions between genes were infectious to tobacco. TVCV with a TMV MP gene infected turnips. The other tested chimeras were not detected in non-inoculated leaves, but were found in the inoculated leaves. Thus, the TMV MP is not responsible for the limitation of TMV spread in turnips.
Brassica↗
[35 years of research and study in radiovirology at the Stefan S. Nicolau Institute of Virology].
The report presents researches conducted in the field of radiovirology, these 35 last years, at the Radiovirology Central Laboratory of the Academy of Medical Sciences: ionizing radiation little dose effects on the evolution of virus infections, virus migration through the infected organism and its stocks in different organs, intracellular synthesis of viruses, radioisotope characterization of viral nucleic acids, studies of viral molecular biology, radioimmunologic diagnosis of virus diseases, virus inactivation and sterilization through ionizing radiation, space virology studies within "Intercosmos" research program.
Academies and Institutes↗
Evidence for human immunodeficiency virus type 1 replication in vivo in CD14(+) monocytes and its potential role as a source of virus in patients on highly active antiretroviral therapy.
In vitro studies show that human immunodeficiency virus type 1 (HIV-1) does not replicate in freshly isolated monocytes unless monocytes differentiate to monocyte-derived macrophages. Similarly, HIV-1 may replicate in macrophages in vivo, whereas it is unclear whether blood monocytes are permissive to productive infection with HIV-1. We investigated HIV-1 replication in CD14(+) monocytes and resting and activated CD4(+) T cells by measuring the levels of cell-associated viral DNA and mRNA and the genetic evolution of HIV-1 in seven acutely infected patients whose plasma viremia had been <100 copies/ml for 803 to 1,544 days during highly active antiretroviral therapy (HAART). HIV-1 DNA was detected in CD14(+) monocytes as well as in activated and resting CD4(+) T cells throughout the course of study. While significant variation in the decay slopes of HIV-1 DNA was seen among individual patients, viral decay in CD14(+) monocytes was on average slower than that in activated and resting CD4(+) T cells. Measurements of HIV-1 sequence evolution and the concentrations of unspliced and multiply spliced mRNA provided evidence of ongoing HIV-1 replication, more pronounced in CD14(+) monocytes than in resting CD4(+) T cells. Phylogenetic analyses of HIV-1 sequences indicated that after prolonged HAART, viral populations related or identical to those found only in CD14(+) monocytes were seen in plasma from three of the seven patients. In the other four patients, HIV-1 sequences in plasma and the three cell populations were identical. CD14(+) monocytes appear to be one of the potential in vivo sources of HIV-1 in patients receiving HAART.
Amino Acid Sequence↗
[Nature and mechanisms of changes in cells during neoplastic evolution].
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Animals↗
[New possibility of genetic characterization of human papillomavirus in pathology of male and female genitalia].
Several epidemiologic studies point to the role of different sublines of Human Papillomavirus (HPV) in the development of neoplasias of the genito-rectal tract. The spread of the virus in the population makes it necessary to constantly investigate this pathogen in order to adopt a correct therapeutic approach and follow the evolution of associated disease. This paper gives an epidemiologic outline of HPV infection in the adult population--males and females--based on a correlated study of the relationship between the lesion and the presence of the virus and its sublines. The methods used both traditional examinations (colposcopy, cytology, histology) and innovative chemiluminescence molecular biology techniques. Chemiluminescence molecular hybridization includes the use of RNA probes which, on the basis the identification of different viral strains, allow a subdivision of infections into low and high/medium risk. The test resulted positive in 60.7% of the cases in which there was clinical and cyto-histopathological evidence of HPV infection. Notwithstanding the high percentage of negative results in the cases of condylomatous disease, the method used has proved to be easily applicable and more sensitive than other molecular biology techniques (comparison by in situ hybridization and Southern blot analysis). Moreover, from the clinical point of view, it seems to provide useful data for a correct diagnosis and monitoring of patients.
Adolescent↗
HIV-resistance evolution requires new strategies. Mutation risk higher if HIV RNA increases.
A new study finds that 60% of HIV patients on stable therapy with detectable viral replication have a rate of new HIV mutations of about 1.5 mutations per year.
Drug Resistance, Viral↗
Real-time reverse transcription-polymerase chain reaction assays for the detection and differentiation of North American swine influenza viruses.
Swine influenza is an acute respiratory disease of swine caused by type A influenza viruses. Before 1998, mainly "classical" HIN1 swine influenza viruses (SIVs) were isolated from swine in the United States. Since then, antigenically distinct reassortant H3 and H1 SIVs have been identified as causative agents of respiratory disease in pigs on US farms. Improvement in SIV diagnostics is needed in light of the recently observed rapid evolution of H1 and H3 SIVs and their zoonotic potential. To address this need, real-time reverse transcription-polymerase chain reaction (RT-PCR) assays for the detection of SIVs were developed. A highly sensitive matrix (M) gene-based RT-PCR assay that is able to detect both the H1 and H3 subtypes of SIVs, with a sensitivity per reaction of approximately 2 copies of in vitro-generated M-specific negative-sense RNA molecules and approximately 0.05 TCID50 in lung lavage of experimentally SIV-infected pigs, was established. This RT-PCR assay can be performed within a few hours and showed a sensitivity of 94% and a specificity of 85% when compared with virus isolation. In addition, H1-, H3-, N1-, and N2-specific primer and probe sets were designed for use in the differentiation of different SIV subtypes. The hemagglutinin (H)- and neuraminidase (N)-specific primer and probe sets were less sensitive than the M-specific assay, although they were found to be specific for their respective viral genes and able to distinguish between their respective SIV subtypes.
Animals↗
RNA silencing of rotavirus gene expression.
RNA interference (RNAi) is a double-stranded RNA (dsRNA)-triggered mechanism for suppressing gene expression, which is conserved in evolution and has emerged as a powerful tool to study gene function. Rotaviruses, the leading cause of severe diarrhea in young children, are formed by three concentric layers of protein, and a genome composed of 11 segments of dsRNA. Here, we show that the RNAi machinery can be triggered to silence rotavirus gene expression by sequence-specific short interfering RNAs (siRNAs). RNAi is also useful for the study of the virus-cell interactions, through the silencing of cellular genes that are potentially important for the replication of the virus. Interestingly, while the translation of mRNAs is readily stopped by the RNAi machinery, the viral transcripts involved in virus genome replication do not seem to be susceptible to RNAi. Since gene silencing by RNAi is very efficient and specific, this system could become a novel therapeutic approach for rotavirus and other virus infections, once efficient methods for in vivo delivery of siRNAs are developed. Although the use of RNAi as an antiviral therapeutic tool remains to be demonstrated, there is no doubt that this technology will influence drastically the way postgenomic virus research is conducted.
Gene Expression Regulation, Viral↗
A map of the diversity of RNA3 recombinants appearing in plants infected with Cucumber mosaic virus and Tomato aspermy virus.
In order to better understand the role of recombination in creating the diversity of viral genomes that is acted on by selection, we have studied in detail the population of recombinant RNA3 molecules occurring in tobacco plants coinfected with wild-type strains of cucumber mosaic virus (CMV) and tomato aspermy virus (TAV) under conditions of minimal selection pressure. Recombinant RNA3s were observed in 9.6% of the samples. Precise homologous recombination predominated since it was observed at 28 different sites, primarily in six hot spots. Imprecise homologous recombination was observed at two sites, particularly within a GU repeat in the 5' noncoding region. Seven of the eight aberrant homologous recombination sites observed were clustered in the 3' noncoding region. These results have implications on the role of recombination in host adaptation and virus evolution. They also provide essential baseline information for understanding the potential epidemiological impact of recombination in transgenic plants expressing viral sequences.
Base Sequence↗
Evolution of cytotoxic T lymphocyte responses to human immunodeficiency virus type 1 in patients with symptomatic primary infection receiving antiretroviral triple therapy.
The impact of highly active antiretroviral treatment (HAART) on anti-human immunodeficiency virus (HIV) cytotoxic T lymphocytes (CTL) was studied in 17 patients with recent symptomatic HIV-1 primary infection receiving triple combination therapy. Anti-HIV CTL were initially detected in 15 patients. In 6, CTL disappeared rapidly and persistently after initiation of therapy. Most of them had a rapid and sustained decrease in plasma HIV RNA to undetectable levels. Conversely, in 6 other patients, CTL remained detectable, which was associated with a less efficient control of viral replication. In 3 others, CTL disappeared only transiently, without clear correlation with the virologic profile. Altogether, despite individual variations, there was a positive correlation between viral replication and anti-HIV-1 cytotoxicity in most subjects, suggesting that the persistence of viral antigens is the main determinant for the maintenance of CTL activity. This raises the question of the potential benefit of anti-HIV CTL induction by immunotherapy in acute seroconverters treated by HAART.
Anti-HIV Agents↗
The antigenicity and evolution of influenza H1 haemagglutinin, from 1950-1957 and 1977-1983: two pathways from one gene.
Nucleotide sequence analysis of the region of the haemagglutinin gene coding for the HA1 domain of the protein was performed on 19 human influenza A strains of H1 subtype representative of the two epidemic periods from 1977-1983 and from 1950-1957. The amino acid changes relative to A/USSR/90/77 are summarised and are consistent with the view that variation in these field strains involves changes largely at the Sb and Ca antigenic sites previously characterised in laboratory mutants of the haemagglutinin of influenza A/PR/8/34. The Sa and Cb sites are less variant and are probably masked by carbohydrate side chains. We discuss the significance of other amino acid changes which do not correspond to previously defined antigenic sites. We also define the "mainstream" amino acid changes characteristic of the divergent evolutionary pathways of the 1950-1957 and 1977-1983 periods and note that the rate of evolution is faster in the earlier period.
Antigens, Viral↗
The origin of cells: a symbiosis between genes, catalysts, and membranes.
The gap between early molecular evolution and the origin of the first cell may have been bridged by a photoheterotrophic obcell, consisting of genes and ribosomes attached to the outer surface of a phospholipid vesicle containing a light-driven proton pump and a proton-driven pyrophosphate synthase. I argue that the obcell was the substratum for the origin of DNA replication; DNA segregation by the growth and division of the peptidoglycan murein; periplasmic solute-binding proteins; bioenergetics, including the F0F1 proton-driven ATP synthase; active transport of calcium; and facilitated diffusion of nutrients across membranes, and that it played the major role in the replacement of ribozymes by protein catalysts. Curved growth of the peptidoglycan and a mutation causing septum formation produced the first true cell. Evolution of porins, sodium extrusion and potassium import, conversion of the facilitated diffusion proteins to active pumps, and the evolution of intermediary metabolism, carbon and nitrogen fixation, and of substrate level phosphorylation, completed the origin of the first negibacterial eubacterium, from which all other cells evolved, and from which they have inherited most of their major catalytic properties--with the notable exceptions of reverse transcriptase, RNA splicing, and methanogenesis, all of which I believe evolved very much later.
Animals↗
Genetic study of Japanese encephalitis viruses from Vietnam.
Two hundred eighty-five nucleotides from the capsid/premembrane gene region of 16 isolates of Japanese encephalitis (JE) virus from the southern and northern regions of Vietnam obtained during the period 1964-1988 were sequenced and compared with each other and with wild JE virus strains from China and Japan. The 16 Vietnamese isolates showed low rates of genetic evolution (< or = 3.2%) and were classified into one genotype with an overall similarity of > or = 95.4%, including the Japanese JaArOS982 strain taken as reference, and earlier isolated strains from Japan (Nakayama 1935) and China (Beijing-1 1949 and SA14 1954), the wild-type strains used to derive JE vaccines. The implications of the close genetic relationship among Vietnamese strains of JE virus analyzed in our study in relation to their epidemiology and evolution are discussed.
Aedes↗
The clinical importance of the nomenclature, evolution and taxonomy of human papillomaviruses.
Human papillomaviruses (HPVs) are formally described by isolation of their circular double-stranded DNA genomes and establishment and comparison of the nucleotide sequence of these genomes. Alternatives such as serological diagnosis and maintenance of HPVs in culture are neither clinically useful nor consistently feasible. Novel HPV isolates have traditionally been described as "types". The analysis of specific HPV types is of medical importance, because HPV types typically induce type-specific lesions, i.e. they may be specific for cutaneous or mucosal epithelia, or give rise to benign warts or malignant carcinomas. Recently, it was formally decided that papillomaviruses are a virus family separate from the polyomaviruses. Within the papillomavirus family, closely or remotely related types form species or genera. These formal agreements were important as they brought the taxonomy of papillomaviruses in line with that of other viruses, bacteria and higher organisms, although their impact on medical practice and terminology used in clinical studies is limited. Notably, however, HPV types that are closely related (i.e. form "species") are associated with similar lesions. Confusion of the terms "type" and "subtype" should be avoided, as the latter term refers to some specific but rare taxonomic assemblages. In contrast to many RNA viruses, HPV types evolve very slowly, and diverged since the origin of humans only by about 2%. These divergent isolates are called "variants". HPVs evolved together with humankind and Homo sapiens was never without HPVs, and consequently never without warts and cervical cancer. Variants of the same HPV type may have different pathogenicity and may account for part of the worldwide disparities in the occurrence of genital cancers.
Evolution, Molecular↗